Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017641.1 Corchorus olitorius cultivar O-4 contig17674, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 69112
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2455 original size:68 final size:68
Alignment explanation
Indices: 2092--2781 Score: 642
Period size: 68 Copynumber: 10.5 Consensus size: 68
2082 AGTAAAGTTC
* * *
2092 TATTTTCTATTTCCAAAAATACCCTTTTGGTCGAAGGGTTATTTT-GTCTTCTCGCATTTAAGTT
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
*
2156 TAA
66 TAG
* * * *
2159 TACTTTCTTTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGCCTT-TTGCATTTAAGTC
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
2223 TAG
66 TAG
* * *
2226 TGTTTTCTATTTCCAAAAATACCCTTTCGGT--AATGGGCCATTTTCGTCTTCTTGCATATAAG-
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAA-GGGTCATTTTCGTCTTCTTGCATTTAAGT
* *
2288 CT-C
65 TTAG
* * * *
2291 CATTTTCTATTTCCGAAAATACCCTTTCGGTCGAAGGGTCATTTTCATCCTT-TTGCATTTGAGT
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGT-CTTCTTGCATTTAAGT
2355 TTA-
65 TTAG
* * * * * * *
2358 -CTTTT-GATTTCCAAAAATACCCTTTCGGTCGAAAGGTCGTTTTTGTCTCCTTGCATTTGAGTT
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
2421 TAG
66 TAG
* *
2424 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCGTTTTTGTCTTCTTGCATTTAAGTT
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
2489 TAG
66 TAG
* * * * *
2492 TATTTTCTATTTTCAAAAATACCCTTTCGGACGAAGGGTCATTTTCGTCTTTTTGCGTTTTAGTT
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
2557 TAG
66 TAG
* * * **
2560 -------TATTTCCAAAAATGCCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGTACCTAAGTT
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
2618 TAG
66 TAG
* * * * * * ** * *
2621 TACTTTCTTTTTCCAAAAATGCCCTTTCGGTCGAAGTGCCAATTTCAACTT-TTCCATATCCAAG
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCAT-T-TAAG
2685 -TTAG
64 TTTAG
* * * * * *
2689 --TTTACT-TTTCCCAAAATACCCTTTCAGTCAAAGGGTCAATTTT-GTCATTTTTGCATTTGAG
1 TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTC-ATTTTCGTC-TTCTTGCATTTAAG
2750 TTTA-
64 TTTAG
* * *
2754 -CTTTT-GATTACC-AAAATACCCTTTCGGT
1 TATTTTCTATTTCCAAAAATACCCTTTCGGT
2782 GAAAAGGTCA
Statistics
Matches: 516, Mismatches: 80, Indels: 56
0.79 0.12 0.09
Matches are distributed among these distances:
61 53 0.10
64 2 0.00
65 123 0.24
66 61 0.12
67 110 0.21
68 164 0.32
69 3 0.01
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (68 bp):
TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCATTTAAGTT
TAG
Found at i:2580 original size:197 final size:194
Alignment explanation
Indices: 2090--2753 Score: 669
Period size: 197 Copynumber: 3.4 Consensus size: 194
2080 AAAGTAAAGT
* * * *
2090 TCTATTTTCTATTTCCAAAAATACCCTTTTGGTCGAAGGGTTATTTT-GTCTTCTCGCATTTAAG
1 TCTATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAAG
*
2154 TTTAATACTTTCTTTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGCCTTTTGCATTTA
66 TTTAATA-------TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCATTTA
* *
2219 AGTCTAGTGTTTTCTATTTCCAAAAATACCCTTTCGGT--AATGGGCCATTTTCGTCTTCTTGCA
124 AGTTTAGTATTTTCTATTTCCAAAAATACCCTTTCGGTCGAA-GGGCCATTTTCGTCTTCTTGCA
2282 TATAAGC
188 TATAAGC
* * * * *
2289 TCCATTTTCTATTTCCGAAAATACCCTTTCGGTCGAAGGGTCATTTTCATCCTTTTGCATTTGAG
1 TCTATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAAG
* * * * * *
2354 TTTACTTTTGATTTCCAAAAATACCCTTTCGGTCGAAAGGTCGTTTTTGTCTCCTTGCATTTGAG
66 TTTA---AT-ATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCT-TTTGCATTTAAG
* * * *
2419 TTTAGTATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCGTTTTTGTCTTCTTGCATTT
126 TTTAGTATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGCCATTTTCGTCTTCTTGCATAT
*
2484 AAGTT
191 AAG-C
* * * * *
2489 TAGTATTTTCTATTTTCAAAAATACCCTTTCGGACGAAGGGTCATTTTCGTCTTTTTGCGTTTTA
1 T-CTATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAA
* * * **
2554 GTTTAGTATTTCCAAAAATGCCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGTACCTAAGTTT
65 GTTTAATATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC-TTTTGCATTTAAGTTT
* * * * * ** *
2619 AGTACTTTCTTTTTCCAAAAATGCCCTTTCGGTCGAAGTGCCAATTTCAACTT-TTCCATATCCA
129 AGTATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGCCATTTTCGTCTTCTTGCATAT--A
2683 AG-
192 AGC
* * * *
2685 T-TAGTTTACT-TTTCCCAAAATACCCTTTCAGTCAAAGGGTCAATTTT-GTCATTTTTGCATTT
1 TCTA-TTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTC-ATTTTCGTC-TTTTTGCATTT
*
2747 GAGTTTA
63 AAGTTTA
2754 CTTTTGATTA
Statistics
Matches: 387, Mismatches: 62, Indels: 36
0.80 0.13 0.07
Matches are distributed among these distances:
194 31 0.08
195 26 0.07
196 7 0.02
197 127 0.33
198 49 0.13
199 67 0.17
200 19 0.05
201 59 0.15
203 1 0.00
204 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (194 bp):
TCTATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAAG
TTTAATATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTGCATTTAAGTTTAG
TATTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGCCATTTTCGTCTTCTTGCATATAAGC
Found at i:2618 original size:61 final size:61
Alignment explanation
Indices: 2499--2656 Score: 181
Period size: 61 Copynumber: 2.5 Consensus size: 61
2489 TAGTATTTTC
* * * *** *
2499 TATTTTCAAAAATACCCTTTCGGACGAAGGGTCATTTTCGTCTTTTTGCGTTTTAGTTTAG
1 TATTTCCAAAAATGCCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCACCTAAGTTTAG
*
2560 TATTTCCAAAAATGCCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGTACCTAAGTTTAG
1 TATTTCCAAAAATGCCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCACCTAAGTTTAG
2621 TACTTTCTTTTTCCAAAAATGCCCTTTCGGTCGAAG
1 TA-------TTTCCAAAAATGCCCTTTCGGTCGAAG
2657 TGCCAATTTC
Statistics
Matches: 82, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
61 55 0.67
68 27 0.33
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.42
Consensus pattern (61 bp):
TATTTCCAAAAATGCCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCACCTAAGTTTAG
Found at i:2673 original size:129 final size:129
Alignment explanation
Indices: 2168--2673 Score: 357
Period size: 129 Copynumber: 3.9 Consensus size: 129
2158 ATACTTTCTT
* ** * **
2168 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGCCTT-TTGCATTTAAGTCTAGTGTTTT
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCACCTAAGTTTAGTACTTT
* * * ** * * * *
2232 CTATTTCCAAAAATACCCTTTCGGTA--ATGGGCCATTTTCGTCTTCTTGCATATAAGCTCCATT
66 CTATTTTCAAAAATACCCTTTCGG-ACGAAGGGCCAATTTCAACTTTTTGCGTTTTAG-----TT
**
2295 TTCTA
125 TAGTA
* * ** *
2300 TTTCCGAAAATACCCTTTCGGTCGAAGGGTCATTTTCATCCTT-TTGCATTTGAG-TT--TACTT
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGT-CTTCTTGCACCTAAGTTTAGTACTT
* * * *** ** *
2361 T-TGATTTCCAAAAATACCCTTTCGGTCGAAAGGTCGTTTTTGTCTCCTTGCATTTGAG-TTTAG
65 TCT-ATTTTCAAAAATACCCTTTCGGACG-AAGGGC-CAATT-TCAACTT---TTTGCGTTTTAG
**
2424 TATTTTCTA
123 --TTTAGTA
* * ** *
2433 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCGTTTTTGTCTTCTTGCATTTAAGTTTAGTATTTT
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCACCTAAGTTTAGTACTTT
* * **
2498 CTATTTTCAAAAATACCCTTTCGGACGAAGGGTCATTTTCGTCTTTTTGCGTTTTAGTTTAGTA
66 CTATTTTCAAAAATACCCTTTCGGACGAAGGGCCAATTTCAACTTTTTGCGTTTTAGTTTAGTA
* * *
2562 TTTCCAAAAATGCCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGTACCTAAGTTTAGTACTTT
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCACCTAAGTTTAGTACTTT
* * *
2627 CT-TTTTCCAAAAATGCCCTTTCGGTCGAAGTGCCAATTTCAACTTTT
66 CTATTTT-CAAAAATACCCTTTCGGACGAAGGGCCAATTTCAACTTTT
2674 CCATATCCAA
Statistics
Matches: 305, Mismatches: 52, Indels: 37
0.77 0.13 0.09
Matches are distributed among these distances:
128 4 0.01
129 98 0.32
130 31 0.10
131 5 0.02
132 44 0.14
133 74 0.24
134 10 0.03
135 4 0.01
136 31 0.10
137 4 0.01
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.43
Consensus pattern (129 bp):
TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTCTTGCACCTAAGTTTAGTACTTT
CTATTTTCAAAAATACCCTTTCGGACGAAGGGCCAATTTCAACTTTTTGCGTTTTAGTTTAGTA
Found at i:2689 original size:129 final size:129
Alignment explanation
Indices: 2168--2743 Score: 332
Period size: 129 Copynumber: 4.4 Consensus size: 129
2158 ATACTTTCTT
* ** * **
2168 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCG-CCTTTTGCATTTAAGTCTAGTGTTTT
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTT-GTCTTTTTGCACCTAAGTTTAGTACTTT
* * * ** * *
2232 CTATTTCCAAAAATACCCTTTCGGTA--ATGGGCCATTTTCGTCTTCTTGCATAT-AAGCTCCAT
65 CTATTTTCAAAAATACCCTTTCGG-ACGAAGGGCCAATTTCAACTTTTTCCAT-TCAAG-T---T
*
2294 T-TTCTA
124 TAGT-TA
* * * ** *
2300 TTTCCGAAAATACCCTTTCGGTCGAAGGGTCATTTTCATCCTTTTGCATTTGAG-TT--TACTTT
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTT-GTCTTTTTGCACCTAAGTTTAGTACTTT
* * * * ** *** ** * **
2362 -TGATTTCCAAAAATACCCTTTCGGTCGAAAGGTCGTTTTTGTCTCCTTGCATTTGAGTTTAGTA
65 CT-ATTTTCAAAAATACCCTTTCGGACGAAGGGCCAATTTCAACTTTTTCCATTCAAGTTTAG--
2426 TTTTCTA
127 ---T-TA
* * ** *
2433 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCGTTTTTGTCTTCTTGCATTTAAGTTTAGTATTTT
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTC-ATTTTGTCTTTTTGCACCTAAGTTTAGTACTTT
* * ** * * **
2498 CTATTTTCAAAAATACCCTTTCGGACGAAGGGTCATTTTCGTCTTTTTGCGTTTTAGTTTAG-TA
65 CTATTTTCAAAAATACCCTTTCGGACGAAGGGCCAATTTCAACTTTTTCCATTCAAGTTTAGTTA
* *
2562 TTTCCAAAAATGCCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGTACCTAAGTTTAGTACTTT
1 TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTT-GTCTTTTTGCACCTAAGTTTAGTACTTT
* * *
2627 CT-TTTTCCAAAAATGCCCTTTCGGTCGAAGTGCCAATTTCAAC-TTTTCCATATCCAAG-TTAG
65 CTATTTT-CAAAAATACCCTTTCGGACGAAGGGCCAATTTCAACTTTTTCCAT-T-CAAGTTTAG
2689 TTTA
127 -TTA
* * *
2693 CTTTTCCCAAAATACCCTTTCAGTCAAAGGGTCAATTTTGTCATTTTTGCA
1 --TTTCCAAAAATACCCTTTCGGTCGAAGGGTC-ATTTTGTC-TTTTTGCA
2744 TTTGAGTTTA
Statistics
Matches: 364, Mismatches: 54, Indels: 50
0.78 0.12 0.11
Matches are distributed among these distances:
127 2 0.01
128 14 0.04
129 92 0.25
130 30 0.08
131 23 0.06
132 37 0.10
133 91 0.25
134 18 0.05
136 56 0.15
137 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.15, T:0.42
Consensus pattern (129 bp):
TTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTGTCTTTTTGCACCTAAGTTTAGTACTTTC
TATTTTCAAAAATACCCTTTCGGACGAAGGGCCAATTTCAACTTTTTCCATTCAAGTTTAGTTA
Found at i:2833 original size:65 final size:66
Alignment explanation
Indices: 2695--2850 Score: 165
Period size: 65 Copynumber: 2.4 Consensus size: 66
2685 TTAGTTTACT
* * * ** ** *
2695 TTTCCCAAAATACCCTTTCAGTCAAAGGGTCAATTTTGTCATTTTTGCATTTGAGTTTACTTTTG
1 TTTCCCAAAATACCCTTTCGGTGAAAAGGTCAATTTCATCATTTCCGCATTTGAGTTTACTTCTG
2760 A
66 A
* * *
2761 -TTACCAAAATACCCTTTCGGTGAAAAGGTCAGTTTCATCATTTCCGCATTTTAGTTTA-TTCT-
1 TTTCCCAAAATACCCTTTCGGTGAAAAGGTCAATTTCATCATTTCCGCATTTGAGTTTACTTCTG
2823 A
66 A
* *
2824 CTTTCCCAAAATGCTCTTTCGGTGAAA
1 -TTTCCCAAAATACCCTTTCGGTGAAA
2851 GGGCAAGCTT
Statistics
Matches: 74, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
63 1 0.01
64 3 0.04
65 70 0.95
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (66 bp):
TTTCCCAAAATACCCTTTCGGTGAAAAGGTCAATTTCATCATTTCCGCATTTGAGTTTACTTCTG
A
Found at i:8216 original size:2 final size:2
Alignment explanation
Indices: 8209--8238 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
8199 GAAGGACCAT
*
8209 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8239 GATAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:8380 original size:10 final size:10
Alignment explanation
Indices: 8353--8389 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
8343 TTCAAATGAA
8353 GGAGGGGT-G
1 GGAGGGGTAG
8362 GGAGGGGTAG
1 GGAGGGGTAG
*
8372 GGTGGGGTAG
1 GGAGGGGTAG
8382 GGAGGGGT
1 GGAGGGGT
8390 TGCAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 8 0.32
10 17 0.68
ACGTcount: A:0.14, C:0.00, G:0.73, T:0.14
Consensus pattern (10 bp):
GGAGGGGTAG
Found at i:22451 original size:22 final size:22
Alignment explanation
Indices: 22423--23418 Score: 344
Period size: 22 Copynumber: 44.9 Consensus size: 22
22413 TCATTGAAGT
*
22423 AAATTGAAGCTTTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
*
22445 AAATTGAAGCATTAAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
* *
22467 AATTTGAAGCATTGAAGAATGG
1 AAATTGAAGCATTGAAGAATTG
* *
22489 AACTTGAAGCATTAAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
* *
22511 AATTTGAAGCATTGAAGAATCG
1 AAATTGAAGCATTGAAGAATTG
* **
22533 AATTTGAAGCATTGACA-TTTTG
1 AAATTGAAGCATTGA-AGAATTG
* *
22555 AATTTGAAGAATTG-A-AATTG
1 AAATTGAAGCATTGAAGAATTG
* * *
22575 AAGCGTTGACA-CTTTG-A-ATTTG
1 AA--ATTGA-AGCATTGAAGAATTG
**
22597 AAGAATTGAA--ATTGAAGCGTTG
1 -A-AATTGAAGCATTGAAGAATTG
22619 AAATTGAAGCATT-AA-AATACTG
1 AAATTGAAGCATTGAAGAAT--TG
*
22641 AAATTGAATCATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
* *
22663 AAATTGAAGTATTGACA-TATTG
1 AAATTGAAGCATTGA-AGAATTG
* *
22685 AAATTGTAA-CATTAAAGGATTG
1 AAATTG-AAGCATTGAAGAATTG
* * *
22707 AATTTGAGGAATTG-A-AATTG
1 AAATTGAAGCATTGAAGAATTG
**
22727 AAGCATTGAAATATTG-A-AATTG
1 AA--ATTGAAGCATTGAAGAATTG
* *
22749 AAACATTGAAGAATTG-A-ATTTG
1 -AA-ATTGAAGCATTGAAGAATTG
*
22771 AATAATTGAA--ATTGAAGCATTG
1 -A-AATTGAAGCATTGAAGAATTG
22793 AAATATTGAA--ATTGAA-ACATTG
1 -AA-ATTGAAGCATTGAAGA-ATTG
*
22815 AAGAATTGAA--TTTG-AGAAATTG
1 -A-AATTGAAGCATTGAAG-AATTG
22837 AAATTGAAGCATTGAA-ATATTG
1 AAATTGAAGCATTGAAGA-ATTG
*
22859 AAATTGAAACATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
* * *
22881 AATTTGAAG-AATCAA-AATTG
1 AAATTGAAGCATTGAAGAATTG
* * *
22901 AAGAGTTTAAGAATTG-A-ATTTG
1 AA-A-TTGAAGCATTGAAGAATTG
* * *
22923 AAGAATCAA-AATTGAAGAATTG
1 AA-ATTGAAGCATTGAAGAATTG
*
22945 AAGAATTGAAGCATTGAA-ATACTG
1 -A-AATTGAAGCATTGAAGA-ATTG
*
22969 AAATTGAATCATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
22991 AAATTGAAGCATTG--GCATATTG
1 AAATTGAAGCATTGAAG-A-ATTG
* *
23013 AAATTGAAACATTGAAGGATTG
1 AAATTGAAGCATTGAAGAATTG
* * * * *
23035 AATTTGGAGAATTGAA-ATTTA
1 AAATTGAAGCATTGAAGAATTG
**
23056 AGAATTGAAATATTG-A-AATTG
1 A-AATTGAAGCATTGAAGAATTG
*
23077 AAACATTGAAGAATTGAATTTGTAGAATTG
1 -AA-ATTGAAGCATTG-A-----AGAATTG
23107 AAATTGAAGCATTGAA-ATATTG
1 AAATTGAAGCATTGAAGA-ATTG
*
23129 AAGAATTGAA--TTTGAAGAATTG
1 -A-AATTGAAGCATTGAAGAATTG
23151 AAGAATTGAA--ATTGAA-ACATTG
1 -A-AATTGAAGCATTGAAGA-ATTG
* ** *
23173 AATATGGAA--ATCAAAGCATTG
1 AA-ATTGAAGCATTGAAGAATTG
* *
23194 AAGAATTTAA--ATTGAAGTATTG
1 -A-AATTGAAGCATTGAAGAATTG
*
23216 AAGAATTGACA-TATTG-A-AATTG
1 -A-AATTGA-AGCATTGAAGAATTG
*
23238 AAACATTGAAGGATTGACCTTGGAGAATTG
1 -AA-ATTGAAGCATTGA------AGAATTG
23268 AAATTGAA--ATTGAA-ACATTG
1 AAATTGAAGCATTGAAGA-ATTG
*
23288 AAGGATTGAA--TTTGAAGAATTG
1 AA--ATTGAAGCATTGAAGAATTG
* *
23310 AAATTGAAACATTGGAA-TATTG
1 AAATTGAAGCATT-GAAGAATTG
23332 AAATTGAAGCATTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
* *
23354 AATTTGAAGCGTTGAAGAATTG
1 AAATTGAAGCATTGAAGAATTG
* *
23376 AATTTGAAGAATTGAA-ATATTG
1 AAATTGAAGCATTGAAGA-ATTG
*
23398 AGTAATTGAAGAATTGAAGAA
1 A--AATTGAAGCATTGAAGAA
23419 AGGCCACTCT
Statistics
Matches: 769, Mismatches: 113, Indels: 182
0.72 0.11 0.17
Matches are distributed among these distances:
19 1 0.00
20 61 0.08
21 52 0.07
22 540 0.70
23 34 0.04
24 41 0.05
25 1 0.00
26 5 0.01
27 1 0.00
28 17 0.02
29 6 0.01
30 10 0.01
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.31
Consensus pattern (22 bp):
AAATTGAAGCATTGAAGAATTG
Found at i:22482 original size:44 final size:44
Alignment explanation
Indices: 22426--23418 Score: 500
Period size: 44 Copynumber: 23.4 Consensus size: 44
22416 TTGAAGTAAA
* *
22426 TTGAAGCTTTGAAGAATTGAAATTGAAGCATTAAAGAATTGAAT
1 TTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAGAATTGAAT
* * *
22470 TTGAAGCATTGAAGAATGGAACTTGAAGCATTAAAGAATTGAAT
1 TTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAGAATTGAAT
* * *
22514 TTGAAGCATTGAAGAATCGAATTTGAAGCATTG-A-CA-T---T
1 TTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAGAATTGAAT
* * **
22552 TTGAA--TTTGAAGAATTGAAATTGAAGCGTTGACA-CTTTGAAT
1 TTGAAGCATTGAAGAATTGAAATTGAAGCATTGA-AGAATTGAAT
* *
22594 TTGAAGAATTGAAATTGAAGCGTTGAAATTGAAGCATT-AA-AATACTGAAA
1 TTGAAGCATTG-AA--GAA---TTGAAATTGAAGCATTGAAGAAT--TGAAT
* * * *
22644 TTGAATCATTGAAGAATTGAAATTGAAGTATTGACA-TATTGAAA
1 TTGAAGCATTGAAGAATTGAAATTGAAGCATTGA-AGAATTGAAT
* * * *
22688 TTGTAA-CATT--A-AA--G-GATTGAA--TTTGAGGAATTGAAA
1 TTG-AAGCATTGAAGAATTGAAATTGAAGCATTGAAGAATTGAAT
*
22724 TTGAAGCATTGAA-ATATTGAAATTGAAACATTGAAGAATTGAAT
1 TTGAAGCATTGAAGA-ATTGAAATTGAAGCATTGAAGAATTGAAT
*
22768 TTG-A--A-T----AATTGAAATTGAAGCATTGAA-ATATTGAAA
1 TTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAGA-ATTGAAT
* * *
22804 TTGAAACATTGAAGAATTG-AATT--TG-A--G-A-AATTGAAA
1 TTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAGAATTGAAT
*
22840 TTGAAGCATTGAA-ATATTGAAATTGAAACATTGAAGAATTGAAT
1 TTGAAGCATTGAAGA-ATTGAAATTGAAGCATTGAAGAATTGAAT
* * *
22884 TTGAAG-AATCAA-AATTG-AA--G-AG--TTTAAGAATTGAAT
1 TTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAGAATTGAAT
* *
22920 TTGAAGAATCAAAATTGAAGAATTGAAGAATTGAAGCATTGAA-ATACTGAAA
1 TTGAAG---C---ATTGAAGAATTG-A-AATTGAAGCATTGAAGA-ATTGAAT
* *
22972 TTGAATCATTGAAGAATTGAAATTGAAGCATTG--GCATATTGAAA
1 TTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAG-A-ATTGAAT
* * *
23016 TTGAAACATTGAAG----G--ATTGAA--TTTGGAGAATTGAAAT
1 TTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAGAATTG-AAT
* *
23053 TT-AAGAATTGAA-ATATTGAAATTGAAACATTGAAGAATTGAAT
1 TTGAAGCATTGAAGA-ATTGAAATTGAAGCATTGAAGAATTGAAT
* * **
23096 TTGTAGAATTG-A-AATTGAAGCATTGAAATATTGAAGAATTGAAT
1 TTGAAGCATTGAAGAATTGAA--ATTGAAGCATTGAAGAATTGAAT
* * * * *
23140 TTGAAGAATTGAAGAATTGAAATTGAAACATTGAA-TATGGAAA
1 TTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAGAATTGAAT
** * *
23183 TCAAAGCATTGAAGAATTTAAATTGAAGTATTGAAGAATTGACAT
1 TTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAGAATTGA-AT
* * *
23228 ATTGAA--ATTGAA-ACATTGAAGGATTG-A-CCTTGGAGAATTGAAA
1 -TTGAAGCATTGAAGA-ATTGAA--ATTGAAGCATTGAAGAATTGAAT
* *
23271 TTGAA--ATTGAA-ACATTGAAGGATTGAA--TTTGAAGAATTGAAA
1 TTGAAGCATTGAAGA-ATTGAA--ATTGAAGCATTGAAGAATTGAAT
* *
23313 TTGAAACATTGGAA-TATTGAAATTGAAGCATTGAAGAATTGAAT
1 TTGAAGCATT-GAAGAATTGAAATTGAAGCATTGAAGAATTGAAT
* * * *
23357 TTGAAGCGTTGAAGAATTGAATTTGAAGAATTGAA-ATATTGAGTAA
1 TTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAGA-ATTGA--AT
*
23403 TTGAAGAATTGAAGAA
1 TTGAAGCATTGAAGAA
23419 AGGCCACTCT
Statistics
Matches: 760, Mismatches: 90, Indels: 196
0.73 0.09 0.19
Matches are distributed among these distances:
35 4 0.01
36 125 0.16
37 13 0.02
38 25 0.03
39 5 0.01
40 6 0.01
41 8 0.01
42 80 0.11
43 64 0.08
44 314 0.41
45 12 0.02
46 44 0.06
47 8 0.01
48 2 0.00
49 5 0.01
50 30 0.04
51 1 0.00
52 14 0.02
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.31
Consensus pattern (44 bp):
TTGAAGCATTGAAGAATTGAAATTGAAGCATTGAAGAATTGAAT
Found at i:22496 original size:58 final size:57
Alignment explanation
Indices: 22423--23415 Score: 374
Period size: 58 Copynumber: 16.4 Consensus size: 57
22413 TCATTGAAGT
*
22423 AAATTGAAGCTTTGAAGAATTGAAATTGAAGCATTAAAGAATTGAATTTGAAGCATTGAAGA
1 AAATTGAA-C-TTGAAGAATTGAAATTGAAGCATTGAAGAATTGAATTTGAAGCATT---GA
* * *
22485 ATGGAACTTGAAGCATTAAAGAATTGAATTTGAAGCATTGAAGAATCGAATTTGAAGCATTGA
1 A---AA-TTGAA-C-TTGAAGAATTGAAATTGAAGCATTGAAGAATTGAATTTGAAGCATTGA
** * * ** *
22548 CATTTTGAATTTGAAGAATTGAAATTGAAGCGTTGACA-CTTTGAATTTGAAGAATTG-
1 -AAATTGAACTTGAAGAATTGAAATTGAAGCATTGA-AGAATTGAATTTGAAGCATTGA
* * *
22605 AAATTGAA---G-CG--TTGAAATTGAAGCATT-AA-AATACTGAAATTGAATCATTGA
1 AAATTGAACTTGAAGAATTGAAATTGAAGCATTGAAGAAT--TGAATTTGAAGCATTGA
* * * * * *
22656 AGAATTGAAATTGAAGTATTGACATATTGAAATTGTAACATTAAAGGATTGAATTTGAGGAATTG
1 A-AATTGAACTTGAAGAATTGA-A-ATTG-AA--G---CATTGAAGAATTGAATTTGAAGCATTG
22721 -
57 A
* **
22721 AAATTGAAGCATTGAA-ATATTGAAATTGAAACATTGAAGAATTGAATTTGAATAATTG-
1 AAATTGAA-C-TTGAAGA-ATTGAAATTGAAGCATTGAAGAATTGAATTTGAAGCATTGA
* *
22779 AAATTGAAGCATTGAA-ATATTGAAATTGAAACATTGAAGAATTGAATTTG-AGAAATTG-
1 AAATTGAA-C-TTGAAGA-ATTGAAATTGAAGCATTGAAGAATTGAATTTGAAG-CATTGA
* * *
22837 AAATTGAAGCATTGAA-ATATTGAAATTGAAACATTGAAGAATTGAATTTGAAG-AATCA
1 AAATTGAA-C-TTGAAGA-ATTGAAATTGAAGCATTGAAGAATTGAATTTGAAGCATTGA
* * * *
22895 AAATTGAAGAGTTTAAGAATTGAATTTGAAGAATCAAAATTGAAGAATTGAAGAATTGAAGCATT
1 AAATTG-A-ACTTGAAGAATTGAAATTGAAG---C---ATTGAAGAATTG-A-ATTTGAAGCATT
22960 GAAATA
56 G----A
* *
22966 CTGAAATTGAATCATTGAAGAATTGAAATTGAAGCATTG--GCATATTGAAATTGAAACATTGA
1 ---AAATTGAA-C-TTGAAGAATTGAAATTGAAGCATTGAAG-A-ATTGAATTTGAAGCATTGA
* * * * * * *
23028 AGGATTGAATTTGGAGAATTGAAATTTAAGAATTGAA-ATATTGAAATTGAAACATTGA
1 A-AATTGAACTTGAAGAATTGAAATTGAAGCATTGAAGA-ATTGAATTTGAAGCATTGA
* * *
23086 AGAATTGAATTTGTAGAATTGAAATTGAAGCATTGAAATATTGAAGAATTGAATTTGAAGAATTG
1 A-AATTGAACTTGAAGAATTGAAATTGAAGC--------ATTGAAGAATTGAATTTGAAGCATTG
23151 A
57 A
* ** * * *
23152 AGAATTGAAATTGAAACATTGAATATGGAAATCAAAGCATTGAAGAATTTAAATTGAAGTATTG-
1 A-AATTGAACTTG--A-A--GAAT-T-GAAATTGAAGCATTGAAGAATTGAATTTGAAGCATTGA
* * * ** * *
23216 -AA--GAA-TTGACA-TATTGAAATTGAAACATTGAAGGATTGACCTTGGAGAATTG-
1 AAATTGAACTTGA-AGAATTGAAATTGAAGCATTGAAGAATTGAATTTGAAGCATTGA
* * * *
23268 AAATTGAAATTGAA-ACATTGAAGGATTGAA--TTTGAAGAATTGAAATTGAAACATTGGAATA
1 AAATTGAACTTGAAGA-ATTGAA--ATTGAAGCATTGAAGAATTGAATTTGAAGCATT-G---A
* * *
23329 TTGAAATTGAAGCATTGAAGAATTGAATTTGAAGCGTTGAAGAATTGAATTTGAAGAATTGA
1 ---AAATTGAA-C-TTGAAGAATTGAAATTGAAGCATTGAAGAATTGAATTTGAAGCATTGA
*
23391 AATATTGAGTAATTGAAGAATTGAA
1 AA-ATTGA--ACTTGAAGAATTGAA
23416 GAAAGGCCAC
Statistics
Matches: 739, Mismatches: 95, Indels: 196
0.72 0.09 0.19
Matches are distributed among these distances:
48 2 0.00
49 1 0.00
50 28 0.04
51 1 0.00
52 36 0.05
53 4 0.01
54 2 0.00
55 5 0.01
56 35 0.05
57 7 0.01
58 267 0.36
59 12 0.02
60 37 0.05
61 3 0.00
62 6 0.01
63 5 0.01
64 37 0.05
65 29 0.04
66 161 0.22
67 8 0.01
68 10 0.01
69 1 0.00
71 6 0.01
72 2 0.00
73 10 0.01
74 24 0.03
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.31
Consensus pattern (57 bp):
AAATTGAACTTGAAGAATTGAAATTGAAGCATTGAAGAATTGAATTTGAAGCATTGA
Found at i:23163 original size:14 final size:14
Alignment explanation
Indices: 22588--23393 Score: 380
Period size: 14 Copynumber: 56.5 Consensus size: 14
22578 CGTTGACACT
*
22588 TTGAATTTGAAGAA
1 TTGAAATTGAAGAA
**
22602 TTGAAATTGAAGCG
1 TTGAAATTGAAGAA
*
22616 TTGAAATTGAAGCA
1 TTGAAATTGAAGAA
*
22630 TTAAAATACTG-A-AA
1 TTGAAAT--TGAAGAA
22644 TTGAATCATTGAAGAA
1 TTGAA--ATTGAAGAA
*
22660 TTGAAATTGAAGTA
1 TTGAAATTGAAGAA
22674 TTGACATATTG-A-AA
1 TTGA-A-ATTGAAGAA
* *
22688 TTGTAACATTAAAGGA
1 TTG-AA-ATTGAAGAA
* *
22704 TTGAATTTGAGGAA
1 TTGAAATTGAAGAA
*
22718 TTGAAATTGAAGCA
1 TTGAAATTGAAGAA
22732 TTGAAATATTG-A-AA
1 TTG-AA-ATTGAAGAA
22746 TTGAAACATTGAAGAA
1 TTG-AA-ATTGAAGAA
* *
22762 TTGAATTTGAATAA
1 TTGAAATTGAAGAA
*
22776 TTGAAATTGAAGCA
1 TTGAAATTGAAGAA
22790 TTGAAATATTG-A-AA
1 TTG-AA-ATTGAAGAA
22804 TTGAAACATTGAAGAA
1 TTG-AA-ATTGAAGAA
*
22820 TTGAATTTG-AGAAA
1 TTGAAATTGAAG-AA
*
22834 TTGAAATTGAAGCA
1 TTGAAATTGAAGAA
22848 TTGAAATATTG-A-AA
1 TTG-AA-ATTGAAGAA
22862 TTGAAACATTGAAGAA
1 TTG-AA-ATTGAAGAA
*
22878 TTGAATTTGAAGAA
1 TTGAAATTGAAGAA
**
22892 TCAAAATTGAAG-A
1 TTGAAATTGAAGAA
*
22905 --G---TTTAAGAA
1 TTGAAATTGAAGAA
*
22914 TTGAATTTGAAGAA
1 TTGAAATTGAAGAA
**
22928 TCAAAATTGAAGAA
1 TTGAAATTGAAGAA
*
22942 TTGAAGAATTGAAGCA
1 TTG-A-AATTGAAGAA
22958 TTGAAATACTG-A-AA
1 TTGAAAT--TGAAGAA
22972 TTGAATCATTGAAGAA
1 TTGAA--ATTGAAGAA
*
22988 TTGAAATTGAAGCA
1 TTGAAATTGAAGAA
*
23002 TTGGCATATTG-A-AA
1 TT-G-AAATTGAAGAA
*
23016 TTGAAACATTGAAGGA
1 TTG-AA-ATTGAAGAA
* *
23032 TTGAATTTGGAGAA
1 TTGAAATTGAAGAA
*
23046 TTGAAATTTAAGAA
1 TTGAAATTGAAGAA
23060 TTGAAATATTG-A-AA
1 TTG-AA-ATTGAAGAA
23074 TTGAAACATTGAAGAA
1 TTG-AA-ATTGAAGAA
* *
23090 TTGAATTTGTAGAA
1 TTGAAATTGAAGAA
*
23104 TTGAAATTGAAGCA
1 TTGAAATTGAAGAA
23118 TTGAAATATTGAAGAA
1 TTG-AA-ATTGAAGAA
*
23134 TTGAATTTGAAGAA
1 TTGAAATTGAAGAA
23148 TTGAAGAATTG-A-AA
1 TTG-A-AATTGAAGAA
*
23162 TTGAAACATTGAA-TA
1 TTG-AA-ATTGAAGAA
* ** *
23177 TGGAAATCAAAGCA
1 TTGAAATTGAAGAA
*
23191 TTGAAGAATT-TA-AA
1 TTG-A-AATTGAAGAA
23205 TTGAAGTATTGAAGAA
1 TTGAA--ATTGAAGAA
23221 TTGACATATTG-A-AA
1 TTGA-A-ATTGAAGAA
*
23235 TTGAAACATTGAAGGA
1 TTG-AA-ATTGAAGAA
** *
23251 TTGACCTTGGAGAA
1 TTGAAATTGAAGAA
23265 TTGAAATTG-A-AA
1 TTGAAATTGAAGAA
*
23277 TTGAAACATTGAAGGA
1 TTG-AA-ATTGAAGAA
*
23293 TTGAATTTGAAGAA
1 TTGAAATTGAAGAA
23307 TTGAAATTGAA-ACA
1 TTGAAATTGAAGA-A
23321 TTGGAATATTG-A-AA
1 TT-GAA-ATTGAAGAA
23335 TTGAAGCATTGAAGAA
1 TTGAA--ATTGAAGAA
*
23351 TTGAATTTGAAG--
1 TTGAAATTGAAGAA
*
23363 -CG---TTGAAGAA
1 TTGAAATTGAAGAA
*
23373 TTGAATTTGAAGAA
1 TTGAAATTGAAGAA
23387 TTGAAAT
1 TTGAAAT
23394 ATTGAGTAAT
Statistics
Matches: 615, Mismatches: 96, Indels: 162
0.70 0.11 0.19
Matches are distributed among these distances:
8 11 0.02
9 1 0.00
11 3 0.00
12 6 0.01
13 18 0.03
14 372 0.60
15 69 0.11
16 134 0.22
17 1 0.00
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.31
Consensus pattern (14 bp):
TTGAAATTGAAGAA
Found at i:23345 original size:8 final size:7
Alignment explanation
Indices: 22434--23391 Score: 183
Period size: 8 Copynumber: 131.7 Consensus size: 7
22424 AATTGAAGCT
22434 TTGAAGAA
1 TTGAAG-A
22442 TTGAA-A
1 TTGAAGA
22448 TTGAAGCA
1 TTGAAG-A
*
22456 TTAAAGAA
1 TTGAAG-A
*
22464 TTGAA-T
1 TTGAAGA
22470 TTGAAGCA
1 TTGAAG-A
22478 TTGAAGAA
1 TTGAAG-A
* *
22486 TGGAA-C
1 TTGAAGA
22492 TTGAAGCA
1 TTGAAG-A
*
22500 TTAAAGAA
1 TTGAAG-A
*
22508 TTGAA-T
1 TTGAAGA
22514 TTGAAGCA
1 TTGAAG-A
22522 TTGAAGAA
1 TTGAAG-A
* *
22530 TCGAA-T
1 TTGAAGA
22536 TTGAAGCA
1 TTGAAG-A
**
22544 TTGACATT
1 TTGA-AGA
*
22552 TTGAA-T
1 TTGAAGA
22558 TTGAAGAA
1 TTGAAG-A
22566 TTGAA-A
1 TTGAAGA
*
22572 TTGAAGCG
1 TTGAAG-A
**
22580 TTGACACT
1 TTGA-AGA
*
22588 TTGAA-T
1 TTGAAGA
22594 TTGAAGAA
1 TTGAAG-A
22602 TTGAA-A
1 TTGAAGA
*
22608 TTGAAGCG
1 TTGAAG-A
22616 TTGAA-A
1 TTGAAGA
22622 TTGAAGCA
1 TTGAAG-A
*
22630 TT-AAAA
1 TTGAAGA
22636 TACTGAA-A
1 T--TGAAGA
*
22644 TTGAATCA
1 TTGAA-GA
22652 TTGAAGAA
1 TTGAAG-A
22660 TTGAA-A
1 TTGAAGA
22666 TTGAAGTA
1 TTGAAG-A
*
22674 TTGACATA
1 TTGA-AGA
22682 TTGAA-A
1 TTGAAGA
*
22688 TTGTAACA
1 TTG-AAGA
*
22696 TTAAAGGA
1 TTGAA-GA
*
22704 TTGAA-T
1 TTGAAGA
*
22710 TTGAGGAA
1 TTGAAG-A
22718 TTGAA-A
1 TTGAAGA
22724 TTGAAGCA
1 TTGAAG-A
*
22732 TTGAAATA
1 TTG-AAGA
22740 TTGAA-A
1 TTGAAGA
*
22746 TTGAAACA
1 TTG-AAGA
22754 TTGAAGAA
1 TTGAAG-A
*
22762 TTGAA-T
1 TTGAAGA
*
22768 TTGAATAA
1 TTGAA-GA
22776 TTGAA-A
1 TTGAAGA
22782 TTGAAGCA
1 TTGAAG-A
*
22790 TTGAAATA
1 TTG-AAGA
22798 TTGAA-A
1 TTGAAGA
*
22804 TTGAAACA
1 TTG-AAGA
22812 TTGAAGAA
1 TTGAAG-A
*
22820 TTGAA-T
1 TTGAAGA
*
22826 TTGAGAAA
1 TTGA-AGA
22834 TTGAA-A
1 TTGAAGA
22840 TTGAAGCA
1 TTGAAG-A
*
22848 TTGAAATA
1 TTG-AAGA
22856 TTGAA-A
1 TTGAAGA
*
22862 TTGAAACA
1 TTG-AAGA
22870 TTGAAGAA
1 TTGAAG-A
*
22878 TTGAA-T
1 TTGAAGA
22884 TTGAAGA
1 TTGAAGA
* * *
22891 ATCAAAA
1 TTGAAGA
22898 TTGAAGA
1 TTGAAGA
*
22905 GTTTAAGAA
1 -TTGAAG-A
*
22914 TTGAA-T
1 TTGAAGA
22920 TTGAAGA
1 TTGAAGA
* * *
22927 ATCAAAA
1 TTGAAGA
22934 TTGAAGAA
1 TTGAAG-A
22942 TTGAAGAA
1 TTGAAG-A
22950 TTGAAGCA
1 TTGAAG-A
22958 TTGAA-A
1 TTGAAGA
22964 TACTGAA-A
1 T--TGAAGA
*
22972 TTGAATCA
1 TTGAA-GA
22980 TTGAAGAA
1 TTGAAG-A
22988 TTGAA-A
1 TTGAAGA
22994 TTGAAGCA
1 TTGAAG-A
* *
23002 TTGGCATA
1 TT-GAAGA
23010 TTGAA-A
1 TTGAAGA
*
23016 TTGAAACA
1 TTG-AAGA
23024 TTGAAGGA
1 TTGAA-GA
*
23032 TTGAA-T
1 TTGAAGA
*
23038 TTGGAGAA
1 TTGAAG-A
23046 TTGAA-A
1 TTGAAGA
*
23052 TTTAAGAA
1 TTGAAG-A
*
23060 TTGAAATA
1 TTG-AAGA
23068 TTGAA-A
1 TTGAAGA
*
23074 TTGAAACA
1 TTG-AAGA
23082 TTGAAGAA
1 TTGAAG-A
*
23090 TTGAA-T
1 TTGAAGA
*
23096 TTGTAGAA
1 TTGAAG-A
23104 TTGAA-A
1 TTGAAGA
23110 TTGAAGCA
1 TTGAAG-A
*
23118 TTGAAATA
1 TTG-AAGA
23126 TTGAAGAA
1 TTGAAG-A
*
23134 TTGAA-T
1 TTGAAGA
23140 TTGAAGAA
1 TTGAAG-A
23148 TTGAAGAA
1 TTGAAG-A
23156 TTGAA-A
1 TTGAAGA
*
23162 TTGAAACA
1 TTG-AAGA
*
23170 TTGAATA
1 TTGAAGA
*
23177 TGGAA-A
1 TTGAAGA
**
23183 TCAAAGCA
1 TTGAAG-A
23191 TTGAAGAA
1 TTGAAG-A
*
23199 TTTAA-A
1 TTGAAGA
23205 TTGAAGTA
1 TTGAAG-A
23213 TTGAAGAA
1 TTGAAG-A
*
23221 TTGACATA
1 TTGA-AGA
23229 TTGAA-A
1 TTGAAGA
*
23235 TTGAAACA
1 TTG-AAGA
23243 TTGAAGGA
1 TTGAA-GA
**
23251 TTG-ACC
1 TTGAAGA
*
23257 TTGGAGAA
1 TTGAAG-A
23265 TTGAA-A
1 TTGAAGA
23271 TTGAA-A
1 TTGAAGA
*
23277 TTGAAACA
1 TTG-AAGA
23285 TTGAAGGA
1 TTGAA-GA
*
23293 TTGAA-T
1 TTGAAGA
23299 TTGAAGAA
1 TTGAAG-A
23307 TTGAA-A
1 TTGAAGA
*
23313 TTGAAACA
1 TTG-AAGA
*
23321 TTGGAATA
1 TT-GAAGA
23329 TTGAA-A
1 TTGAAGA
23335 TTGAAGCA
1 TTGAAG-A
23343 TTGAAGAA
1 TTGAAG-A
*
23351 TTGAA-T
1 TTGAAGA
*
23357 TTGAAGCG
1 TTGAAG-A
23365 TTGAAGAA
1 TTGAAG-A
*
23373 TTGAA-T
1 TTGAAGA
23379 TTGAAGAA
1 TTGAAG-A
23387 TTGAA
1 TTGAA
23392 ATATTGAGTA
Statistics
Matches: 717, Mismatches: 117, Indels: 232
0.67 0.11 0.22
Matches are distributed among these distances:
6 221 0.31
7 83 0.12
8 393 0.55
9 20 0.03
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.31
Consensus pattern (7 bp):
TTGAAGA
Found at i:23465 original size:16 final size:16
Alignment explanation
Indices: 23444--23474 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
23434 AATGAAGTAA
*
23444 ATTGAAGCATTGAAGG
1 ATTGAAGAATTGAAGG
23460 ATTGAAGAATTGAAG
1 ATTGAAGAATTGAAG
23475 CTAATTGAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.29, T:0.26
Consensus pattern (16 bp):
ATTGAAGAATTGAAGG
Found at i:30880 original size:43 final size:42
Alignment explanation
Indices: 30823--31068 Score: 203
Period size: 41 Copynumber: 5.8 Consensus size: 42
30813 AGATCCCTAG
*
30823 GTGTTATAAATGTGCTTGAGGACTTTGAGAGAGTGATGCCCCT
1 GTGTTATAAATGTGCTTGAGGACTTTGAGAGAG-GATGCCTCT
* * * *
30866 GTGTTATAATTGTGCTT-AGGGACTTTGATA-TGGATGCTTCT
1 GTGTTATAAATGTGCTTGA-GGACTTTGAGAGAGGATGCCTCT
* * * *
30907 GTGTTTTAAATGTGTTTGAGGACTTTTAG-GAAGGATTGCCCCT
1 GTGTTATAAATGTGCTTGAGGACTTTGAGAG-AGGA-TGCCTCT
* * * * * * *
30950 GTGTTAGAATTGTGTTTGGGGACTTTGACATA-GATGCTTCT
1 GTGTTATAAATGTGCTTGAGGACTTTGAGAGAGGATGCCTCT
* * * *
30991 GTGTTATAAATGTGATTGAGGACTTCAGAAAGAGAGTTGCCTCT
1 GTGTTATAAATGTGCTTGAGGACTT-TGAGAGAG-GATGCCTCT
* *
31035 GTGTTATATATGTGCTTGGGGACTTTGGAGAGAG
1 GTGTTATAAATGTGCTTGAGGACTTT-GAGAGAG
31069 AGAAATGCCC
Statistics
Matches: 157, Mismatches: 36, Indels: 19
0.74 0.17 0.09
Matches are distributed among these distances:
41 55 0.35
42 12 0.08
43 55 0.35
44 35 0.22
ACGTcount: A:0.22, C:0.11, G:0.30, T:0.37
Consensus pattern (42 bp):
GTGTTATAAATGTGCTTGAGGACTTTGAGAGAGGATGCCTCT
Found at i:30896 original size:84 final size:83
Alignment explanation
Indices: 30792--31061 Score: 292
Period size: 84 Copynumber: 3.2 Consensus size: 83
30782 TTGTGTTACA
* * * * ** *
30792 TGTGTTTAGGGACTTAGATATAGATCCCTAGGTGTTATAAATGTGCTTGAGGACTTTGAGAGAGT
1 TGTGCTTAGGGACTTTGATATAGATGCTTCTGTGTTATAAATGTGATTGAGGACTTTGAGAGAG-
30857 GATGCCCCTGTGTTATAAT
65 GATGCCCCTGTGTTATAAT
* * * *
30876 TGTGCTTAGGGACTTTGATATGGATGCTTCTGTGTTTTAAATGTGTTTGAGGACTTTTAG-GAAG
1 TGTGCTTAGGGACTTTGATATAGATGCTTCTGTGTTATAAATGTGATTGAGGACTTTGAGAG-AG
*
30940 GATTGCCCCTGTGTTAGAAT
65 GA-TGCCCCTGTGTTATAAT
* * * * *
30960 TGTGTTTGGGGACTTTGACATAGATGCTTCTGTGTTATAAATGTGATTGAGGACTTCAGAAAGAG
1 TGTGCTTAGGGACTTTGATATAGATGCTTCTGTGTTATAAATGTGATTGAGGACTT-TGAGAGAG
* *
31025 AGTTGCCTCTGTGTTAT-AT
65 -GATGCCCCTGTGTTATAAT
*
31044 ATGTGCTTGGGGACTTTG
1 -TGTGCTTAGGGACTTTG
31062 GAGAGAGAGA
Statistics
Matches: 156, Mismatches: 24, Indels: 11
0.82 0.13 0.06
Matches are distributed among these distances:
83 3 0.02
84 120 0.77
85 31 0.20
86 2 0.01
ACGTcount: A:0.22, C:0.11, G:0.29, T:0.38
Consensus pattern (83 bp):
TGTGCTTAGGGACTTTGATATAGATGCTTCTGTGTTATAAATGTGATTGAGGACTTTGAGAGAGG
ATGCCCCTGTGTTATAAT
Found at i:30930 original size:41 final size:41
Alignment explanation
Indices: 30823--31061 Score: 187
Period size: 43 Copynumber: 5.7 Consensus size: 41
30813 AGATCCCTAG
30823 GTGTTATAAATGTGCTTGAGGACTTTGAGAGAGTGATGCCCCT
1 GTGTTATAAATGTGCTTGAGGACTTTGAGA-AG-GATGCCCCT
* * * **
30866 GTGTTATAATTGTGCTT-AGGGACTTTGATATGGATGCTTCT
1 GTGTTATAAATGTGCTTGA-GGACTTTGAGAAGGATGCCCCT
* * *
30907 GTGTTTTAAATGTGTTTGAGGACTTTTAGGAAGGATTGCCCCT
1 GTGTTATAAATGTGCTTGAGGACTTTGA-GAAGGA-TGCCCCT
* * * * * **
30950 GTGTTAGAATTGTGTTTGGGGACTTTGACATA-GATGCTTCT
1 GTGTTATAAATGTGCTTGAGGACTTTGAGA-AGGATGCCCCT
* * *
30991 GTGTTATAAATGTGATTGAGGAC-TTCAGAAAGAGAGTTGCCTCT
1 GTGTTATAAATGTGCTTGAGGACTTTGAG-AAG-GA--TGCCCCT
* *
31035 GTGTTATATATGTGCTTGGGGACTTTG
1 GTGTTATAAATGTGCTTGAGGACTTTG
31062 GAGAGAGAGA
Statistics
Matches: 153, Mismatches: 32, Indels: 20
0.75 0.16 0.10
Matches are distributed among these distances:
40 4 0.03
41 54 0.35
42 12 0.08
43 55 0.36
44 26 0.17
45 2 0.01
ACGTcount: A:0.22, C:0.11, G:0.29, T:0.38
Consensus pattern (41 bp):
GTGTTATAAATGTGCTTGAGGACTTTGAGAAGGATGCCCCT
Found at i:31482 original size:18 final size:18
Alignment explanation
Indices: 31461--31497 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
31451 ATCCTATTAC
31461 TCATTAAAAGCCCACTAT
1 TCATTAAAAGCCCACTAT
* *
31479 TCATTAGAAGCCCATTAT
1 TCATTAAAAGCCCACTAT
31497 T
1 T
31498 TACAAATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.32
Consensus pattern (18 bp):
TCATTAAAAGCCCACTAT
Found at i:32728 original size:14 final size:14
Alignment explanation
Indices: 32709--32737 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
32699 AGTTATGGGC
32709 TTATATGGGCTGAG
1 TTATATGGGCTGAG
32723 TTATATGGGCTGAG
1 TTATATGGGCTGAG
32737 T
1 T
32738 ATTGATCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.34, T:0.38
Consensus pattern (14 bp):
TTATATGGGCTGAG
Found at i:34517 original size:17 final size:18
Alignment explanation
Indices: 34489--34522 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
34479 CTCCTCTTTC
34489 ATGAAAACACTTCTTTTT
1 ATGAAAACACTTCTTTTT
*
34507 ATGAAAA-ACTTGTTTT
1 ATGAAAACACTTCTTTT
34523 AACTACCCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (18 bp):
ATGAAAACACTTCTTTTT
Found at i:34970 original size:17 final size:17
Alignment explanation
Indices: 34948--34981 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
34938 ATGACTCAAT
34948 TATCAAGCATTCACCCC
1 TATCAAGCATTCACCCC
*
34965 TATCAAGTATTCACCCC
1 TATCAAGCATTCACCCC
34982 CCCACACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.38, G:0.06, T:0.26
Consensus pattern (17 bp):
TATCAAGCATTCACCCC
Found at i:40039 original size:21 final size:21
Alignment explanation
Indices: 40006--40054 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
39996 AAGAATTGTA
**
40006 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCACTCTT
*
40026 GCTTCCTTTGAAATCACTCTT
1 GCTTCCTTGGAAATCACTCTT
40047 GCATTCCT
1 GC-TTCCT
40055 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.16, C:0.27, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCACTCTT
Found at i:41166 original size:27 final size:25
Alignment explanation
Indices: 41136--41191 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
41126 AAAAGTAACT
41136 AAGAAAAATAAACGAAAATAAAAGAAA
1 AAGAAAAAT-AACGAAAA-AAAAGAAA
* *
41163 AAGAAAAATAATGAAAAAAAATAAA
1 AAGAAAAATAACGAAAAAAAAGAAA
41188 AAGA
1 AAGA
41192 TAAGGGTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 11 0.41
26 7 0.26
27 9 0.33
ACGTcount: A:0.79, C:0.02, G:0.11, T:0.09
Consensus pattern (25 bp):
AAGAAAAATAACGAAAAAAAAGAAA
Found at i:42641 original size:18 final size:19
Alignment explanation
Indices: 42608--42645 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
42598 TAGTTTTAGA
*
42608 TCTATTTTTCTCTTCTAGT
1 TCTAGTTTTCTCTTCTAGT
42627 TCTAGTTTT-TCTTCTAGT
1 TCTAGTTTTCTCTTCTAGT
42645 T
1 T
42646 TTAGGGCTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.11, C:0.18, G:0.08, T:0.63
Consensus pattern (19 bp):
TCTAGTTTTCTCTTCTAGT
Found at i:43810 original size:2 final size:2
Alignment explanation
Indices: 43803--43828 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
43793 CGTTTTCAAA
43803 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
43829 TTCTGCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52554 original size:18 final size:19
Alignment explanation
Indices: 52521--52558 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
52511 TAGTTTTAGA
*
52521 TCTATTTTTCTCTTCTAGT
1 TCTAGTTTTCTCTTCTAGT
52540 TCTAGTTTT-TCTTCTAGT
1 TCTAGTTTTCTCTTCTAGT
52558 T
1 T
52559 TTAGGGCTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.11, C:0.18, G:0.08, T:0.63
Consensus pattern (19 bp):
TCTAGTTTTCTCTTCTAGT
Found at i:54667 original size:76 final size:76
Alignment explanation
Indices: 54540--54681 Score: 173
Period size: 76 Copynumber: 1.9 Consensus size: 76
54530 CGACTCCACC
* * *
54540 TGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGGACCCAGGTGGGCAGTGTC
1 TGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGCACCCAGATGGGCAGTGTC
54605 ACAACTCCAGT
66 ACAACTCCAGT
* * * *
54616 TGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCAGATGGGCTGT
1 TGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGCACCCAGATGGGCAGT
54678 GTCA
63 GTCA
54682 TAGCTCATCA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
75 4 0.07
76 46 0.82
77 6 0.11
ACGTcount: A:0.17, C:0.27, G:0.30, T:0.26
Consensus pattern (76 bp):
TGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGCACCCAGATGGGCAGTGTC
ACAACTCCAGT
Found at i:55918 original size:29 final size:29
Alignment explanation
Indices: 55876--56139 Score: 237
Period size: 29 Copynumber: 9.0 Consensus size: 29
55866 CAGAGTCAAT
55876 TCAAAATGACATATAAAAATATAATTAAA
1 TCAAAATGACATATAAAAATATAATTAAA
55905 TCAAAATGACATATAAAAATATAATTAAA
1 TCAAAATGACATATAAAAATATAATTAAA
*
55934 TCAAAATGACGTATAAAAATGACATATAATTAAA
1 TCAAAATGAC--ATATAAA--A-ATATAATTAAA
* * * *
55968 T-ATAATTA-A-ATCAAAATGA-CATATAAA
1 TCAAAATGACATATAAAAAT-ATAAT-TAAA
* * *
55995 --AATAT-A-AT-T--AAATCAAAATGACATA
1 TCAAAATGACATATAAAAAT-ATAATTA-A-A
56020 T-AAAAGTGACATATAATTAAATATAATTAAA
1 TCAAAA-TGACATATAA--AAATATAATTAAA
56051 TCAAAATGACATATAAAAATATAATTAAA
1 TCAAAATGACATATAAAAATATAATTAAA
56080 TCAAAATGACATATAAAAATATAATTAAA
1 TCAAAATGACATATAAAAATATAATTAAA
56109 TCAAAATGACATATAATTAAATATAATTAAA
1 TCAAAATGACATATAA--AAATATAATTAAA
56140 GGAAAAAATG
Statistics
Matches: 198, Mismatches: 14, Indels: 44
0.77 0.05 0.17
Matches are distributed among these distances:
23 6 0.03
24 3 0.02
25 4 0.02
26 10 0.05
27 7 0.04
28 1 0.01
29 102 0.52
30 2 0.01
31 31 0.16
32 5 0.03
33 11 0.06
34 16 0.08
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.29
Consensus pattern (29 bp):
TCAAAATGACATATAAAAATATAATTAAA
Found at i:55978 original size:44 final size:42
Alignment explanation
Indices: 55907--55997 Score: 155
Period size: 44 Copynumber: 2.1 Consensus size: 42
55897 TAATTAAATC
*
55907 AAAATGACATATAAAAATATAATTAAATCAAAATGACGTATA
1 AAAATGACATATAAAAATATAATTAAATCAAAATGACATATA
55949 AAAATGACATATAATTAAATATAATTAAATCAAAATGACATATA
1 AAAATGACATATAA--AAATATAATTAAATCAAAATGACATATA
55993 AAAAT
1 AAAAT
55998 ATAATTAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
42 14 0.30
44 32 0.70
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.27
Consensus pattern (42 bp):
AAAATGACATATAAAAATATAATTAAATCAAAATGACATATA
Found at i:55995 original size:73 final size:73
Alignment explanation
Indices: 55878--56099 Score: 412
Period size: 73 Copynumber: 3.1 Consensus size: 73
55868 GAGTCAATTC
55878 AAAATGACATATAA--AAATATAATTAAATCAAAATGACATATAAAAATATAATTAAATCAAAAT
1 AAAATGACATATAATTAAATATAATTAAATCAAAATGACATATAAAAATATAATTAAATCAAAAT
*
55941 GACGTATA
66 GACATATA
55949 AAAATGACATATAATTAAATATAATTAAATCAAAATGACATATAAAAATATAATTAAATCAAAAT
1 AAAATGACATATAATTAAATATAATTAAATCAAAATGACATATAAAAATATAATTAAATCAAAAT
56014 GACATATA
66 GACATATA
*
56022 AAAGTGACATATAATTAAATATAATTAAATCAAAATGACATATAAAAATATAATTAAATCAAAAT
1 AAAATGACATATAATTAAATATAATTAAATCAAAATGACATATAAAAATATAATTAAATCAAAAT
56087 GACATATA
66 GACATATA
56095 AAAAT
1 AAAAT
56100 ATAATTAAAT
Statistics
Matches: 146, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
71 14 0.10
73 132 0.90
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (73 bp):
AAAATGACATATAATTAAATATAATTAAATCAAAATGACATATAAAAATATAATTAAATCAAAAT
GACATATA
Found at i:56000 original size:102 final size:97
Alignment explanation
Indices: 55876--56139 Score: 384
Period size: 102 Copynumber: 2.6 Consensus size: 97
55866 CAGAGTCAAT
55876 TCAAAATGACATATAAAAATATAATTAAATCAAAATGACATATAAAAATATAATTAAATCAAAAT
1 TCAAAATGACATATAAAAATATAATTAAATCAAAATGACATATAAAAATATAATTAAAT-AAAAT
*
55941 GACGTATAAAAATGACATATAATTAAATATAATTAAA
65 GA--AATAAAAATGACATATAA--AAATATAATTAAA
55978 TCAAAATGACATATAAAAATATAATTAAATCAAAATGACATATAAAAGTGACATATAATTAAATA
1 TCAAAATGACATATAAAAATATAATTAAATCAAAATGACATAT-AAA---A-ATATAATTAAATA
* * *
56043 TAATTAAATCAAAATGACATATAAAAATATAATTAAA
61 AAATGAAATAAAAATGACATATAAAAATATAATTAAA
56080 TCAAAATGACATATAAAAATATAATTAAATCAAAATGACATATAATTAAATATAATTAAA
1 TCAAAATGACATATAAAAATATAATTAAATCAAAATGACATATAA--AAATATAATTAAA
56140 GGAAAAAATG
Statistics
Matches: 151, Mismatches: 4, Indels: 17
0.88 0.02 0.10
Matches are distributed among these distances:
99 11 0.07
100 1 0.01
101 2 0.01
102 99 0.66
103 4 0.03
104 16 0.11
106 6 0.04
107 12 0.08
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.29
Consensus pattern (97 bp):
TCAAAATGACATATAAAAATATAATTAAATCAAAATGACATATAAAAATATAATTAAATAAAATG
AAATAAAAATGACATATAAAAATATAATTAAA
Found at i:56047 original size:44 final size:41
Alignment explanation
Indices: 55980--56068 Score: 151
Period size: 44 Copynumber: 2.1 Consensus size: 41
55970 TAATTAAATC
55980 AAAATGACATATAAAAATATAATTAAATCAAAATGACATAT
1 AAAATGACATATAAAAATATAATTAAATCAAAATGACATAT
56021 AAAAGTGACATATAATTAAATATAATTAAATCAAAATGACATAT
1 AAAA-TGACATATAA--AAATATAATTAAATCAAAATGACATAT
56065 AAAA
1 AAAA
56069 ATATAATTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
41 4 0.09
42 10 0.22
44 31 0.69
ACGTcount: A:0.61, C:0.07, G:0.06, T:0.27
Consensus pattern (41 bp):
AAAATGACATATAAAAATATAATTAAATCAAAATGACATAT
Found at i:58010 original size:15 final size:15
Alignment explanation
Indices: 57990--58022 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
57980 TGGTCAATGA
57990 TTTTCTTTCTTTTC-T
1 TTTTCTTT-TTTTCAT
58005 TTTTCTTTTTTTCAT
1 TTTTCTTTTTTTCAT
58020 TTT
1 TTT
58023 ATGTAAATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCTTTTTTTCAT
Found at i:63338 original size:18 final size:18
Alignment explanation
Indices: 63311--63347 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
63301 CATTTATTAT
* *
63311 TTAATTATTATTGATATA
1 TTAATAATTATTAATATA
63329 TTAATAATTATTAATATA
1 TTAATAATTATTAATATA
63347 T
1 T
63348 ATTATTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTAATAATTATTAATATA
Found at i:65029 original size:31 final size:31
Alignment explanation
Indices: 64991--65077 Score: 120
Period size: 31 Copynumber: 2.8 Consensus size: 31
64981 TTTCAACAAA
* * *
64991 ATTTTAAAAGTTTAGGGGGTAAAATGTTAAG
1 ATTTTAAAAGTTTAGGGGGCAAAATATCAAG
* *
65022 ATTTTAAAAGTTTATGGGGCAAAATATCAAT
1 ATTTTAAAAGTTTAGGGGGCAAAATATCAAG
*
65053 ATTTTAAAAGTTTAGGAGGCAAAAT
1 ATTTTAAAAGTTTAGGGGGCAAAAT
65078 TATTAGATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.34
Consensus pattern (31 bp):
ATTTTAAAAGTTTAGGGGGCAAAATATCAAG
Found at i:65088 original size:31 final size:30
Alignment explanation
Indices: 64991--65088 Score: 110
Period size: 31 Copynumber: 3.2 Consensus size: 30
64981 TTTCAACAAA
*
64991 ATTTTAAAAGTTTAGGGGGTAAAATGT-TAAG
1 ATTTTAAAAGTTTA-GGGGCAAAAT-TATAAG
*
65022 ATTTTAAAAGTTTATGGGGCAAAA-TATCAAT
1 ATTTTAAAAGTTTA-GGGGCAAAATTAT-AAG
*
65053 ATTTTAAAAGTTTAGGAGGCAAAATTATTAG
1 ATTTTAAAAGTTTAGG-GGCAAAATTATAAG
65084 ATTTT
1 ATTTT
65089 TCAAGTCCAC
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
29 1 0.02
30 3 0.05
31 51 0.88
32 3 0.05
ACGTcount: A:0.40, C:0.03, G:0.19, T:0.38
Consensus pattern (30 bp):
ATTTTAAAAGTTTAGGGGCAAAATTATAAG
Found at i:68001 original size:31 final size:31
Alignment explanation
Indices: 67963--68028 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 31
67953 CAGTATCAAT
*
67963 TTTTTTTCATAG-AGAATCATA-AGCAAATTTC
1 TTTTTTTCAAAGAAG-ATCATACA-CAAATTTC
67994 TTTTTTTCAAAGAAGATCATACACAAATTTC
1 TTTTTTTCAAAGAAGATCATACACAAATTTC
68025 TTTT
1 TTTT
68029 GTCAGATTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 29 0.91
32 3 0.09
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.44
Consensus pattern (31 bp):
TTTTTTTCAAAGAAGATCATACACAAATTTC
Found at i:68521 original size:29 final size:31
Alignment explanation
Indices: 68489--68555 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
68479 ATGCAATTTG
68489 GGATATAACGTTAC-AAAA-CAAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
* *
68518 GGATATAATGTTACGAAAAGCGAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
68549 GGATATA
1 GGATATA
68556 GTCCGTTAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 13 0.38
30 4 0.12
31 17 0.50
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.22
Consensus pattern (31 bp):
GGATATAACGTTACGAAAAGCAAGCAATTAA
Found at i:68814 original size:31 final size:31
Alignment explanation
Indices: 68685--68825 Score: 137
Period size: 31 Copynumber: 4.6 Consensus size: 31
68675 CCCTAACTGA
68685 TTATATCCTTAATTGCTTGAAATC-GAAAACG
1 TTATATCCTTAATTGCTTG-AATCAGAAAACG
**
68716 CCATATCCTTAATTGCTTGAAATCA-AAAACG
1 TTATATCCTTAATTGCTTG-AATCAGAAAACG
* ** * *
68747 TTATATCCTTAATTGCTTG-TTTTG-TAACA
1 TTATATCCTTAATTGCTTGAATCAGAAAACG
***
68776 TTATATCCTTAATTGCTTGCGGCAGAAAACG
1 TTATATCCTTAATTGCTTGAATCAGAAAACG
*
68807 TTATATCCTAAATTGCTTG
1 TTATATCCTTAATTGCTTG
68826 CTTATCATCT
Statistics
Matches: 90, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
29 23 0.26
30 1 0.01
31 66 0.73
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (31 bp):
TTATATCCTTAATTGCTTGAATCAGAAAACG
Done.